[BioC] linear model design

[Erica Leder]

Hi,

I am trying to set up my linear model design matrix and contrast matrix 
and I am having some difficulty.  I am using Agilent's one-color 
platform, so I have a matrix of normalized intensity values as my input 
object for lmfit.

I have 3 populations, 12 samples from each population, and a treatment 
that was conducted on 6 individuals from each population (36 arrays 
total).  I am interested in population differences, treatment 
differences, and any population x treatment differences.  I also have 
individuals of both sexes among the samples, so I would like to correct 
for any sex affects in the model.
I am new to linear models, but I thought I understood how to do this 
until I decided to add the sex information to the model.  I would 
greatly appreciate any suggestions.

Thanks,

Erica



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Erica Leder
Division of Genetics and Physiology
Dept of Biology (Vesilinnantie 5)
20014 University of Turku
Finland

mobile +358 509313035
tel.  +358 23337086
fax.  +358 23336680

erica.leder at utu.fi